BPRMeth package submission

[andreaskapou]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/andreaskapou/BPRMeth

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[bioc-issue-bot]

Hi @andreaskapou

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: BPRMeth
Type: Package
Title: Model higher-order methylation profiles
Version: 0.99.0
Authors@R: person("C. A.", "Kapourani", email = "C.A.Kapourani@ed.ac.uk",
        role = c("aut", "cre"))
Author: Chantriolnt-Andreas Kapourani [aut, cre]
Maintainer: Chantriolnt-Andreas Kapourani <C.A.Kapourani@ed.ac.uk>
Description: BPRMeth package uses the Binomial Probit Regression likelihood 
    to model methylation profiles and extract higher order features. These 
    features quantitate precisely notions of shape of a methylation profile. 
    Using these higher order features across promoter-proximal regions, we 
    construct a powerful predictor of gene expression. Also, these features 
    are used to cluster proximal-promoter regions using the EM algorithm.
Depends:
    R (>= 3.3.0),
    GenomicRanges
License: GPL-3
LazyData: true
RoxygenNote: 5.0.1
Imports: assertthat,
    methods,
    MASS,
    doParallel,
    parallel,
    e1071,
    earth,
    foreach,
    randomForest,
    stats,
    IRanges,
    S4Vectors,
    data.table,
    graphics
Suggests: testthat,
    knitr,
    rmarkdown,
    BiocStyle
VignetteBuilder: knitr
biocViews: DNAMethylation,
    GeneExpression,
    GeneRegulation,
    Epigenetics,
    Genetics,
    Clustering,
    FeatureExtraction,
    Regression,
    RNASeq,
    Bayesian,
    KEGG, 
    Sequencing, 
    Coverage

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/BPRMeth_buildreport_20160801193618.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

bbcbbec Update README file b73909e Update doc vignettes f85f0fe Update vignettes 08c2350 Change email of maintainer and update package vers...

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/BPRMeth_buildreport_20160802080130.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

9abe68f Add 4 spaces in the code format 43b923e Add running examples 2a5d26c Add Imports to NAMESPACE so Bioconductor does not ... e6edf89 Remove old files b2d1e39 Update vignette for not running parallel code

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/BPRMeth_buildreport_20160802113658.html

[andreaskapou]

Hi,

This package was written as a support for a paper accepted (arXiv:1603.08386) at the ECCB 2016 which will be held from 3-7 of September, and is also accepted for publication in the Bioinformatics journal.

I will be giving a presentation of my work at the main conference, and it would be great if I could inform them that my method is available through Bioconductor.

I would appreciate it if the review process would be quick enough so as to know about the inclusion of my package before the conference.

Kind Regards, Andreas

---

Chantriolnt - Andreas Kapourani PhD Candidate in Data Science, School of Informatics, University of Edinburgh

e-mail : C.A.Kapourani.ed.ac.uk : kapouranis.andreas@gmail.com

On Tue, Aug 2, 2016 at 4:35 PM, bioc-issue-bot notifications@github.com wrote:

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/BPRMeth_buildreport_ 20160802113658.html

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/74#issuecomment-236943396, or mute the thread https://github.com/notifications/unsubscribe-auth/AJ6_lVH8mpuma7DCDuSsfnbInq3wA9wCks5qb2PPgaJpZM4JaFNS .

[hpages]

Hi Andreas,

I'm sorry for my slow response. The package looks great and I'm marking it as 'accepted'. It'll be added to the BioC svn repository and to the nightly builds, with further instructions sent to you via email in the next several days.

Congratulations and thanks for your contribution to the project.

Cheers, H.

[andreaskapou]

Hi,

Thanks for the acceptance of the package.

Glad to contribute to Bioconductor!

Kind Regards, Andreas

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[andreaskapou]

Hi,

I saw that Bioconductor 3.4 is released, but I cannot find my package there?

I thought that when a package is accepted it is automatically added to the next release of Bioconductor. May I ask you what is wrong here?

I am looking forward to hearing from you!

Regards, Andreas

[andreaskapou]

Hi,

I still cannot find my package on Bioconductor. Is there anything that I should do in order this to happen?

Thanks!